CARS2 (cysteinyl-tRNA synthetase 2, mitochondrial)

Gene

• Entrez ID: 79587
• Gene name: Cysteinyl-tRNA synthetase 2, mitochondrial
• Gene symbol: CARS2
• Synonyms (NCBI Gene): COXPD27, cysRS
• Chromosome: 13
• Chromosome location: 13q34
• Summary: This gene encodes a putative member of the class I family of aminoacyl-tRNA synthetases. These enzymes play a critical role in protein biosynthesis by charging tRNAs with their cognate amino acids. This protein is encoded by the nuclear genome but is like

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs557671802	G>A	Pathogenic	Non coding transcript variant, missense variant, 5 prime UTR variant, coding sequence variant
rs727505361	C>T	Likely-pathogenic, pathogenic	Missense variant, 5 prime UTR variant, non coding transcript variant, coding sequence variant
rs753472937	CTC>-	Pathogenic	5 prime UTR variant, inframe deletion, non coding transcript variant, coding sequence variant
rs1258446331	AA>-	Likely-pathogenic	Non coding transcript variant, frameshift variant, coding sequence variant
rs1412483498	G>-	Likely-pathogenic	Frameshift variant, non coding transcript variant, genic upstream transcript variant, coding sequence variant, intron variant, upstream transcript variant, 5 prime UTR variant
rs1555342802	->T	Pathogenic	Genic downstream transcript variant, coding sequence variant, non coding transcript variant, frameshift variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT020814	hsa-miR-155-5p	Proteomics	18668040
MIRT029604	hsa-miR-26b-5p	Microarray	19088304
MIRT047820	hsa-miR-30d-5p	CLASH	23622248

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000166	Function	Nucleotide binding	IEA
GO:0004812	Function	Aminoacyl-tRNA ligase activity	IEA
GO:0004817	Function	Cysteine-tRNA ligase activity	IBA
GO:0004817	Function	Cysteine-tRNA ligase activity	IEA
GO:0004817	Function	Cysteine-tRNA ligase activity	IMP	29079736
GO:0005524	Function	ATP binding	IBA
GO:0005524	Function	ATP binding	IEA
GO:0005737	Component	Cytoplasm	IBA
GO:0005739	Component	Mitochondrion	HTP	34800366
GO:0005739	Component	Mitochondrion	IDA	29079736
GO:0005739	Component	Mitochondrion	IEA
GO:0006412	Process	Translation	IEA
GO:0006418	Process	TRNA aminoacylation for protein translation	IEA
GO:0006423	Process	Cysteinyl-tRNA aminoacylation	IBA
GO:0006423	Process	Cysteinyl-tRNA aminoacylation	IEA
GO:0006423	Process	Cysteinyl-tRNA aminoacylation	IMP	29079736
GO:0016874	Function	Ligase activity	IEA
GO:0046872	Function	Metal ion binding	IEA

Other IDs

• MIM: 612800
• HGNC: 25695
• e!Ensembl: ENSG00000134905

Protein

• UniProt ID: Q9HA77
• Protein name: Probable cysteine--tRNA ligase, mitochondrial (EC 6.1.1.16) (Cysteinyl-tRNA synthetase) (CysRS)
• Protein function: Mitochondrial cysteine-specific aminoacyl-tRNA synthetase that catalyzes the ATP-dependent ligation of cysteine to tRNA(Cys). ; In addition to its role as an aminoacyl-tRNA synthetase, has also cysteine pe
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF01406	tRNA-synt_1e	65 → 365	tRNA synthetases class I (C) catalytic domain	Family

• Sequence:

  MLRTTRGPGLGPPLLQAALGLGRAGWHWPAGRAASGGRGRAWLQPTGRETGVQVYNSLTG
  RKEPLIVAHAEAASWYSCGPTVYDHAHLGHACSYVRFDIIRRILTKVFGCSIVMVMGITD
  VDDKIIKRANEMNISPASLASLYEEDFKQDMAALKVLPPTVYLRVTENIPQIISFIEGII
  ARGNAYSTAKGNVYFDLKSRGDKYGKLVGVVPGPVGEPADSDKRHASDFALWKAAKPQEV
  FWASPWGPGRPGWHIECSAIASMVFGSQLDIHSGGIDLAFPHHENEIAQCEVFHQCEQWG
  NYFLHSGHLHAKGKEEKMSKSLKNYITIKDFLKTFSPDVFRFFCLRSSYRSAIDYSDSAM
  LQAQQLLLGLGSFLEDARAYMKGQLACGSVREAMLWERLSSTKRAVKAALADDFDTPRVV
  DAILGLAHHGNGQLRASLKEPEGPRSPAVFGAIISYFEQFFETVGISLANQQYVSGDGSE
  ATLHGVVDELVRFRQKVRQFALAMPEATGDARRQQLLERQPLLEACDTLRRGLTAHGINI
  KDRSSTTSTWELLDQRTKDQKSAG

• Sequence length: 564

Pathways

KEGG:

Aminoacyl-tRNA biosynthesis

Associated diseases

Evidence Score:

• ★☆☆☆☆  Gene-disease association found in Text Mining only
• ★★☆☆☆  Found in Text Mining and Unknown/Other Associations
• ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources
• ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants)
• ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Combined oxidative phosphorylation defect type 27	Pathogenic; Likely pathogenic	rs1555342802, rs1887501594	RCV001199369 RCV001249205	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
BONE REMODELING DISEASE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CARS2-related disorder	Conflicting classifications of pathogenicity; Likely benign; Benign; Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cervical cancer	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cholangiocarcinoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Clear cell carcinoma of kidney	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Colon adenocarcinoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
COMBINED OXIDATIVE PHOSPHORYLATION DEFICIENCY 27	—	CTD, HPO CTD, HPO	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DIABETES MELLITUS AUTOSOMAL DOMINANT TYPE II	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Familial cancer of breast	Likely benign; Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Gastric cancer	Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Lung cancer	Benign; Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant tumor of esophagus	Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant tumor of urinary bladder	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Maturity-onset diabetes of the young type 2	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Microcephaly	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MITOCHONDRIAL DISEASE	—	ClinGen, GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MITOCHONDRIAL DISEASES	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Nonpapillary renal cell carcinoma	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Papillary renal cell carcinoma type 1	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PARKINSON DISEASE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Sarcoma	Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Thyroid cancer, nonmedullary, 1	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine carcinosarcoma	Likely benign; Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine corpus endometrial carcinoma	Likely benign; Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Autism Spectrum Disorders	Autism Spectrum Disorder	BEFREE	31724540		★☆☆☆☆ Found in Text Mining only
Autistic behavior	Autism	HPO_DG			★☆☆☆☆ Found in Text Mining only
Autistic Disorder	Autism	BEFREE	31724540		★☆☆☆☆ Found in Text Mining only
Cerebellar Hypoplasia	Cerebellar Hypoplasia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Cerebral atrophy	Cerebral Atrophy	HPO_DG			★☆☆☆☆ Found in Text Mining only
Colorectal Neoplasms	Colorectal neoplasm	Pubtator	36299603	Associate	★☆☆☆☆ Found in Text Mining only
Combined oxidative phosphorylation defect type 27	Combined Oxidative Phosphorylation Deficiency	Orphanet			★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
COMBINED OXIDATIVE PHOSPHORYLATION DEFICIENCY 27	Combined Oxidative Phosphorylation Deficiency	UNIPROT_DG	25361775, 25787132		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
COMBINED OXIDATIVE PHOSPHORYLATION DEFICIENCY 27	Combined Oxidative Phosphorylation Deficiency	ORPHANET_DG	25361775, 25787132		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
COMBINED OXIDATIVE PHOSPHORYLATION DEFICIENCY 27	Combined Oxidative Phosphorylation Deficiency	GENOMICS_ENGLAND_DG	25787132, 30139652		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
COMBINED OXIDATIVE PHOSPHORYLATION DEFICIENCY 27	Combined Oxidative Phosphorylation Deficiency	CLINVAR_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
COMBINED OXIDATIVE PHOSPHORYLATION DEFICIENCY 27	Combined Oxidative Phosphorylation Deficiency	CTD_human_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Deglutition Disorders	Dysphagia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Developmental regression	Developmental regression	HPO_DG			★☆☆☆☆ Found in Text Mining only
Epileptic encephalopathy	Epileptic encephalopathy	BEFREE	25787132		★☆☆☆☆ Found in Text Mining only
Epileptic encephalopathy	Epileptic encephalopathy	HPO_DG			★☆☆☆☆ Found in Text Mining only
Generalized myoclonic seizures	Myoclonic Seizures	HPO_DG			★☆☆☆☆ Found in Text Mining only
Global developmental delay	Developmental Delay	HPO_DG			★☆☆☆☆ Found in Text Mining only
Hydrops Fetalis, Non-Immune	Hydrops Fetalis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Hypoplasia of corpus callosum	Hypoplasia Of Corpus Callosum	HPO_DG			★☆☆☆☆ Found in Text Mining only
Hypoplastic hippocampus	Hypoplastic hippocampus	HPO_DG			★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Mental retardation	HPO_DG			★☆☆☆☆ Found in Text Mining only
Ki-1+ Anaplastic Large Cell Lymphoma	Anaplastic Lymphoma	BEFREE	12112524		★☆☆☆☆ Found in Text Mining only
MERRF Syndrome	MERRF Syndrome	BEFREE	25361775		★☆☆☆☆ Found in Text Mining only
Movement Disorders	Movement Disorders	BEFREE	25787132		★☆☆☆☆ Found in Text Mining only
Myoclonic Epilepsies, Progressive	Myoclonic epilepsy	BEFREE	25361775		★☆☆☆☆ Found in Text Mining only
Parkinson Disease	Parkinson disease	Pubtator	34064523	Associate	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Status Epilepticus	Status Epilepticus	HPO_DG			★☆☆☆☆ Found in Text Mining only
Unverricht-Lundborg Syndrome	Myoclonic Epilepsy	BEFREE	25361775		★☆☆☆☆ Found in Text Mining only